Starting phenix.real_space_refine on Sun Oct 13 10:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/10_2024/7sng_25225_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9632 2.51 5 N 2616 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 15204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 residue: pdb=" N GLU C 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C 504 " occ=0.50 residue: pdb=" N GLU D 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D 504 " occ=0.50 Time building chain proxies: 10.60, per 1000 atoms: 0.70 Number of scatterers: 15204 At special positions: 0 Unit cell: (135.29, 96.28, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2876 8.00 N 2616 7.00 C 9632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 43.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.793A pdb=" N PHE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.735A pdb=" N HIS A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.546A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.746A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.282A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.717A pdb=" N GLU A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.645A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.572A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.891A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 3.810A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.585A pdb=" N TYR B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.809A pdb=" N ASN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.745A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.623A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.531A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.550A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.080A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 47 through 58 Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 3.837A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.612A pdb=" N TYR C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.757A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.250A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.502A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.562A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.042A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 47 through 58 Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.873A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.534A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.692A pdb=" N TYR D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.805A pdb=" N ASN D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.541A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.294A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.521A pdb=" N GLN D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.695A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.604A pdb=" N THR D 319 " --> pdb=" O GLY D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.534A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.046A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.418A pdb=" N ILE A 33 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.449A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 232 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.491A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 421 removed outlier: 6.699A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 232 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.420A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.760A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS C 232 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ILE C 480 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 305 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR C 482 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN C 307 " --> pdb=" O TYR C 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.485A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.719A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 232 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE D 480 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 305 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR D 482 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN D 307 " --> pdb=" O TYR D 482 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2534 1.32 - 1.44: 4163 1.44 - 1.57: 8623 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA LYS D 171 " pdb=" C LYS D 171 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.11e-02 8.12e+03 2.11e+01 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.17e-02 7.31e+03 1.97e+01 bond pdb=" N VAL D 169 " pdb=" CA VAL D 169 " ideal model delta sigma weight residual 1.458 1.407 0.051 1.20e-02 6.94e+03 1.81e+01 bond pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.07e-02 8.73e+03 1.75e+01 bond pdb=" C VAL D 169 " pdb=" O VAL D 169 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.13e-02 7.83e+03 1.47e+01 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 20571 2.20 - 4.41: 280 4.41 - 6.61: 32 6.61 - 8.81: 11 8.81 - 11.02: 2 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 314 " pdb=" CA GLY B 314 " pdb=" C GLY B 314 " ideal model delta sigma weight residual 111.85 117.84 -5.99 1.06e+00 8.90e-01 3.19e+01 angle pdb=" C ASN B 311 " pdb=" N PRO B 312 " pdb=" CA PRO B 312 " ideal model delta sigma weight residual 119.24 113.54 5.70 1.04e+00 9.25e-01 3.00e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" CB GLU D 170 " ideal model delta sigma weight residual 110.85 102.56 8.29 1.60e+00 3.91e-01 2.69e+01 angle pdb=" N GLY B 316 " pdb=" CA GLY B 316 " pdb=" C GLY B 316 " ideal model delta sigma weight residual 113.18 102.16 11.02 2.37e+00 1.78e-01 2.16e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" C GLU D 170 " ideal model delta sigma weight residual 109.95 116.96 -7.01 1.59e+00 3.96e-01 1.94e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8413 17.98 - 35.97: 700 35.97 - 53.95: 135 53.95 - 71.93: 39 71.93 - 89.91: 17 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA MET D 411 " pdb=" C MET D 411 " pdb=" N PHE D 412 " pdb=" CA PHE D 412 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET A 411 " pdb=" C MET A 411 " pdb=" N PHE A 412 " pdb=" CA PHE A 412 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET C 411 " pdb=" C MET C 411 " pdb=" N PHE C 412 " pdb=" CA PHE C 412 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1539 0.040 - 0.080: 496 0.080 - 0.120: 168 0.120 - 0.159: 35 0.159 - 0.199: 2 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA VAL B 309 " pdb=" N VAL B 309 " pdb=" C VAL B 309 " pdb=" CB VAL B 309 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CB VAL D 169 " pdb=" CA VAL D 169 " pdb=" CG1 VAL D 169 " pdb=" CG2 VAL D 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 311 " -0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 312 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO D 312 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 225 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP D 225 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 225 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP D 225 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 225 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 225 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 225 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 225 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 225 " -0.002 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1341 2.74 - 3.28: 15171 3.28 - 3.82: 26513 3.82 - 4.36: 34513 4.36 - 4.90: 56961 Nonbonded interactions: 134499 Sorted by model distance: nonbonded pdb=" O LYS A 47 " pdb=" OG1 THR A 51 " model vdw 2.201 3.040 nonbonded pdb=" O LYS C 47 " pdb=" OG1 THR C 51 " model vdw 2.205 3.040 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.208 3.120 nonbonded pdb=" O LYS D 47 " pdb=" OG1 THR D 51 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.218 3.040 ... (remaining 134494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 36.470 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15452 Z= 0.264 Angle : 0.634 11.017 20896 Z= 0.341 Chirality : 0.045 0.199 2240 Planarity : 0.006 0.098 2732 Dihedral : 14.539 89.913 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 0.25 % Allowed : 0.31 % Favored : 99.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1852 helix: -0.33 (0.21), residues: 684 sheet: -0.80 (0.24), residues: 412 loop : -0.09 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 225 HIS 0.002 0.001 HIS D 451 PHE 0.017 0.001 PHE D 413 TYR 0.038 0.001 TYR D 139 ARG 0.004 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 1.798 Fit side-chains REVERT: C 37 MET cc_start: 0.9070 (mmm) cc_final: 0.8834 (mmt) REVERT: D 244 GLU cc_start: 0.7737 (mp0) cc_final: 0.7516 (mp0) outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 1.3511 time to fit residues: 354.9592 Evaluate side-chains 197 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain D residue 171 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN C 83 GLN C 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15452 Z= 0.450 Angle : 0.692 13.121 20896 Z= 0.354 Chirality : 0.049 0.153 2240 Planarity : 0.006 0.071 2732 Dihedral : 5.208 39.610 2061 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 7.84 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1852 helix: -0.02 (0.20), residues: 708 sheet: -0.92 (0.24), residues: 408 loop : -0.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 225 HIS 0.006 0.001 HIS B 201 PHE 0.026 0.002 PHE D 413 TYR 0.032 0.002 TYR D 139 ARG 0.006 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 1.869 Fit side-chains REVERT: A 258 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7142 (t70) REVERT: A 345 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: A 503 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6827 (t80) REVERT: D 389 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7440 (mt-10) outliers start: 25 outliers final: 9 residues processed: 235 average time/residue: 1.4868 time to fit residues: 382.4147 Evaluate side-chains 216 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 0.0870 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15452 Z= 0.233 Angle : 0.562 6.918 20896 Z= 0.292 Chirality : 0.044 0.149 2240 Planarity : 0.005 0.061 2732 Dihedral : 4.703 28.081 2057 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.35 % Allowed : 12.62 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1852 helix: 0.25 (0.20), residues: 704 sheet: -0.75 (0.26), residues: 368 loop : -0.23 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 164 HIS 0.003 0.001 HIS A 201 PHE 0.014 0.001 PHE D 413 TYR 0.016 0.001 TYR D 139 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.681 Fit side-chains REVERT: A 258 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7009 (t70) REVERT: A 503 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6840 (t80) REVERT: D 389 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7469 (mt-10) outliers start: 22 outliers final: 6 residues processed: 249 average time/residue: 1.5837 time to fit residues: 430.3437 Evaluate side-chains 226 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 384 GLN A 414 ASN B 83 GLN D 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15452 Z= 0.332 Angle : 0.603 7.598 20896 Z= 0.309 Chirality : 0.046 0.143 2240 Planarity : 0.005 0.056 2732 Dihedral : 4.756 24.284 2057 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.59 % Allowed : 15.56 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1852 helix: 0.18 (0.20), residues: 716 sheet: -0.95 (0.24), residues: 412 loop : -0.10 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 53 HIS 0.004 0.001 HIS C 470 PHE 0.018 0.002 PHE D 413 TYR 0.014 0.002 TYR A 401 ARG 0.005 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.476 Fit side-chains REVERT: A 258 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7088 (t70) REVERT: A 383 GLN cc_start: 0.7868 (mp-120) cc_final: 0.7661 (mm-40) REVERT: B 503 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6786 (t80) REVERT: C 142 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8656 (pt) REVERT: C 244 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: D 389 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7449 (mt-10) outliers start: 26 outliers final: 12 residues processed: 231 average time/residue: 1.5937 time to fit residues: 403.7622 Evaluate side-chains 222 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 83 GLN B 451 HIS C 451 HIS D 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15452 Z= 0.210 Angle : 0.542 7.468 20896 Z= 0.281 Chirality : 0.043 0.149 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.512 20.970 2057 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.65 % Allowed : 16.91 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1852 helix: 0.45 (0.20), residues: 716 sheet: -0.91 (0.24), residues: 412 loop : -0.10 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE D 413 TYR 0.013 0.001 TYR A 249 ARG 0.006 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.982 Fit side-chains REVERT: A 258 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6971 (t70) REVERT: C 142 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8651 (pp) REVERT: C 244 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: D 389 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: D 473 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6700 (mp0) outliers start: 27 outliers final: 11 residues processed: 235 average time/residue: 1.4417 time to fit residues: 371.2464 Evaluate side-chains 229 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 83 GLN B 383 GLN B 451 HIS C 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15452 Z= 0.328 Angle : 0.596 8.399 20896 Z= 0.305 Chirality : 0.045 0.151 2240 Planarity : 0.005 0.050 2732 Dihedral : 4.643 20.786 2056 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.65 % Allowed : 17.77 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1852 helix: 0.39 (0.19), residues: 716 sheet: -0.97 (0.23), residues: 448 loop : 0.01 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 53 HIS 0.004 0.001 HIS C 470 PHE 0.017 0.001 PHE C 87 TYR 0.015 0.002 TYR A 401 ARG 0.006 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.967 Fit side-chains REVERT: A 320 LYS cc_start: 0.8221 (mttp) cc_final: 0.7958 (mptt) REVERT: C 142 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8669 (pp) REVERT: C 244 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: D 389 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: D 473 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6726 (mp0) outliers start: 27 outliers final: 13 residues processed: 236 average time/residue: 1.5351 time to fit residues: 398.5915 Evaluate side-chains 223 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 451 HIS C 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15452 Z= 0.225 Angle : 0.548 7.045 20896 Z= 0.283 Chirality : 0.043 0.144 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.471 19.281 2056 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.53 % Allowed : 18.14 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1852 helix: 0.50 (0.20), residues: 716 sheet: -0.91 (0.23), residues: 448 loop : 0.04 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 53 HIS 0.003 0.001 HIS C 470 PHE 0.011 0.001 PHE C 102 TYR 0.014 0.001 TYR B 249 ARG 0.007 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 2.032 Fit side-chains REVERT: A 258 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7033 (t70) REVERT: D 389 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: D 473 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6754 (mp0) outliers start: 25 outliers final: 13 residues processed: 232 average time/residue: 1.5417 time to fit residues: 392.0901 Evaluate side-chains 227 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15452 Z= 0.241 Angle : 0.558 6.491 20896 Z= 0.288 Chirality : 0.044 0.182 2240 Planarity : 0.004 0.049 2732 Dihedral : 4.479 19.907 2056 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.41 % Allowed : 18.69 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1852 helix: 0.50 (0.20), residues: 720 sheet: -0.86 (0.24), residues: 448 loop : 0.08 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 53 HIS 0.003 0.001 HIS D 451 PHE 0.015 0.001 PHE A 102 TYR 0.017 0.001 TYR C 139 ARG 0.007 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 258 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7046 (t70) REVERT: C 244 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: C 317 GLU cc_start: 0.6542 (tt0) cc_final: 0.6238 (tt0) REVERT: D 389 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: D 473 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6786 (mp0) outliers start: 23 outliers final: 13 residues processed: 219 average time/residue: 1.5911 time to fit residues: 382.7665 Evaluate side-chains 220 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 383 GLN C 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15452 Z= 0.181 Angle : 0.533 6.878 20896 Z= 0.275 Chirality : 0.043 0.144 2240 Planarity : 0.004 0.049 2732 Dihedral : 4.327 19.367 2056 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.10 % Allowed : 19.30 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1852 helix: 0.64 (0.20), residues: 716 sheet: -0.73 (0.25), residues: 416 loop : 0.11 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 53 HIS 0.003 0.001 HIS A 201 PHE 0.009 0.001 PHE C 102 TYR 0.017 0.001 TYR B 249 ARG 0.009 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8548 (pt0) cc_final: 0.8334 (pt0) REVERT: D 389 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: D 473 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6782 (mp0) outliers start: 18 outliers final: 9 residues processed: 223 average time/residue: 1.6172 time to fit residues: 396.1226 Evaluate side-chains 211 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 8.9990 chunk 106 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 414 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15452 Z= 0.227 Angle : 0.561 7.985 20896 Z= 0.288 Chirality : 0.043 0.145 2240 Planarity : 0.004 0.049 2732 Dihedral : 4.385 19.481 2056 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 0.98 % Allowed : 19.73 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1852 helix: 0.64 (0.20), residues: 720 sheet: -0.82 (0.24), residues: 456 loop : 0.16 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 53 HIS 0.003 0.001 HIS D 451 PHE 0.012 0.001 PHE C 413 TYR 0.016 0.001 TYR A 249 ARG 0.009 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.970 Fit side-chains REVERT: A 104 ARG cc_start: 0.7525 (ttt90) cc_final: 0.7199 (ttt90) REVERT: D 325 ASP cc_start: 0.7255 (t0) cc_final: 0.6707 (m-30) REVERT: D 389 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: D 473 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6789 (mp0) outliers start: 16 outliers final: 12 residues processed: 214 average time/residue: 1.5210 time to fit residues: 357.4556 Evaluate side-chains 211 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: